Dynamics of a Pig Slurry Microbial Community during Anaerobic Storage and Management

Abstract

The microbial community of a pig slurry on a farm was monitored for 6 months using both molecular and cultural approaches. Sampling was carried out at all the different stages of effluent handling, from the rearing build-up to slurry spreading. Total DNA of each sample was extracted and analyzed by PCR-single-strand conformation polymorphism (SSCP) analysis using primers targeting the 16S rRNA genes from the archaeal and bacterial domains and also the Eubacterium-Clostridium, Bacillus-Streptococcus-Lactobacillus, and Bacteroides-Prevotella groups. A comparison of the SSCP profiles showed that there were rapid changes in the dominant bacterial community during the first 2 weeks of anaerobic storage and that the community was relatively stable thereafter. Several bacterial populations, identified as populations closely related to uncultured Clostridium and Porphyromonas and to Lactobacillus and Streptococcus cultured species commonly isolated from pig feces, remained present and dominant from the rearing build-up to the time of spreading. Enumeration of fecal indicators (enterococci and Escherichia coli) performed in parallel using cultural methods revealed the same trends. On the other hand, the archaeal community adapted slowly during pig slurry storage, and its diversity increased. A shift between two hydrogenotrophic methanogenic Methanobrevibacter populations from the storage pit to the pond was observed. Microorganisms present in pig slurry at the time of spreading could not be detected in soil after spreading by either molecular or cultural techniques, probably because of the detection limit inherent in the two techniques.

Identification of Methanoculleus spp. as Active Methanogens during Anoxic Incubations of Swine Manure Storage Tank Samples

“…and Methanoculleus spp. In terms of the abundant genera, the archaeal community in this storage tank was similar to previously characterized communities (6)(7)(8).…”

“…as the dominant archaea associated with stored pig manure (6)(7)(8). However, manure storage tanks are similar to fed-batch bioreactors fed with communities indigenous to fresh manure, which are not necessarily active in the environmental conditions of storage tanks.…”

Pig Manure Contamination Marker Selection Based on the Influence of Biological Treatment on the Dominant Fecal Microbial Groups

“…Molecular markers have been developed to target the 16S rRNA gene sequences of dominant Eubacteria (2,14,43,48) or methanogenic Archaebacteria (54) of the pig intestinal tract, whereas Khatib et al (29) targeted the STII toxin gene from enterotoxigenic E. coli. Among the dominant groups of pig fecal Eubacteria, which include Bacteroides-Prevotella, Eubacterium-Clostridiacea, Lactobacillus-Streptococcus (34,45,51,58), and to a lesser extent Bifidobacterium (40), the Bacteroides-Prevotella group has been particularly well studied (14,22,44). This marker of pig feces was described by Okabe et al (44), but their work was based on feces sampled from only two farms and the number of clones analyzed was low.…”

Effect of Bacillus spp. direct-fed microbial on slurry characteristics and gaseous emissions in growing pigs fed with high fibre-based diets

“…Yet, replacement of Methanobrevibacter spp. by other archaeal species such as Methanosarcina, and Methanoculleus representatives has been demonstrated to occur spontaneously in swine manure storage tanks (Peu et al, 2006;Barret et al, 2013).…”

“…DFM on microbial interactions was difficult to analyse (Figure 4). The main identified microbial groups, for example Bacteroidetes, Bacilli, Clostridia encompass most of known fermentative bacteria in pig manure (Peu et al, 2006) as well as in anaerobic digesters (Liu et al, 2009;Riviere et al, 2009). …”